Main
Chun-Hui Gao (高春辉)
Ph. D, Microbiology, bioinformatician, data scientist and R user.
I am broadly interested in the data mining, particularly integration and visualization, of biological, industrial and social datasets, which comes from high-throughput screening, Next-Generation Sequqncing (NGS), public databases and so on.
Work Experience
Post-doc Lecturer
College of Resources and Environment
Huazhong Agricultural University
2019 - 2016
Post-doctoral Fellow
School of Life Science
University of Science and Technology of China
2015 - 2013
Lecturer
School of Food and Biological Engineering
Hubei University of Technology
2012
Education
PhD., Microbiology
Huazhong Agricultural University
Wuhan, CN
2012 - 2007
- Thesis: The characterization of a novel ArsR-type regulator in Mycobacterium tuberculosis and the characterization of molecular basis of isoniazid drug resistance in Mycobacteria
B. S., Biotechnology
Huazhong Agricultural University
Wuhan, CN
2008 - 2004
- bachelor-master continous program
The SCELSE Summer Course
Singapore Centre for Environmental Life Sciences Engineering
Singapore, SG
2016
土壤微生物新理论新技术研讨会暨培训班
中科院南京土壤所
Nanjing, CN
2018/11/17 - 2018/11/15
“不忘初心,牢记使命”教工党员培训班
韶山干部培训学院
Shaoshan, CN
2018
Research Summary
Professional Competence
Microbiology
- Transcriptional regulator
- Drug resistance
- Pathogenisis
- Persistance
Microbial ecology
- Social interaction
- Co-culture
- Multispecies biofilm
NGS
- (meta-)Genomics
- (meta-)RNA-seq
- Microbiome
- ChIP-seq
Bioinformatics
- Linux
- Perl
- R
Visualization
- ggplot2
- ggVennDiagram
- Reproducible research
Skills
- Write R package
- Statistics
- Illustration
- Bibliometric
- Data mining
Whole genome protein-protein and TF-promoter interactome in M. tuberculosis
College of Life Science and Technology
Huazhong Agricultural University
2007 - 2009
We used a bacterial two-hybrid method to construct the whole genome protein-protein interaction (PPI) network, and a bacterial one-hybrid method to construct the whole genome transcriptional regulator (TF) - promoter interaction network in M. tuberculosis.
Novel transcriptional regulator in mycobacteria
College of Life Science and Technology
Huazhong Agricultural University
2009 - 2012
- An ArsR-like transcriptional factor recognizes a conserved sequence motif and positively regulates the expression of phoP in mycobacteria
- A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis
- Characterization of a Novel ArsR-Like Regulator Encoded by Rv2034 in Mycobacterium tuberculosis
The intra-action between three RelBE modules and inter-action between RelBE3/SirR
College of Life Science and Technology
Huazhong Agricultural University
2009 - 2014
- Characterization of the Interaction and Cross-Regulation of Three Mycobacterium tuberculosis RelBE Modules.
- Characterization of the interaction between a SirR family transcriptional factor of Mycobacterium tuberculosis, encoded by Rv2788, and a pair of toxin-antitoxin proteins RelJ/K, encoded by Rv3357 and Rv3358.
The regulation of secondary metabolite (ε-poly lysine) biosynthesis in Streptomyces albus ZPM
School of Life Science
University of Science and Technology of China
2013 - 2014
- Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.
The distribution of type III-A CRISPR-Cas system in Staphylococcus aureus clinical isolates
School of Life Science
University of Science and Technology of China
2014 - 2015
- Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus.
The regulatory mechanism of drug susceptibility in mycobacteria
State Key Laboratory of Agricultural Microbiology
Huazhong Agricultural University
2012 - 2019
- InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
- OxiR specifically responds to isoniazid and regulates isoniazid susceptibility in mycobacteria
- Cross-talk between the three furA orthologs in Mycobacterium smegmatis and the contribution to isoniazid resistance
Unearthing the mechanism of soil biofilms
College of Resources and Environment
Huazhong Agricultural University
2016 - 2019
- Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides
- Co-culture of soil biofilm isolates enables the discovery of novel antibiotics
- Divergent Influence to a Pathogen Invader by Resident Bacteria with Different Social Interactions
- Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization
- Impact of metal oxide nanoparticles on in vitro DNA amplification
Teaching Experience
RNA-seq从入门到精通
华中农业大学暑期生物信息学培训班
武汉
2018/7/18
土壤生物化学课题组导师宣讲会
undergraduate students
Wuhan, CN
2018/6/8
土壤微生物组
undergraduate students
Wuhan, CN
2018/5/24
土壤中的多物种生物膜
graduated students
Wuhan, CN
2016/12/1
Conferences
Oral presentations
细菌的江湖——土壤微生物互作研究
华中农业大学资源与环境学院博士后交流会
武汉
2018/9/11
微生物之间的协作有利于细菌的存活和代谢
全国土壤生物生化与土壤健康学术研讨会
上海
2017
土壤生物膜的形成和群落演替
中国土壤学会第十三次全国会员代表大会
西安
2016
Conference abstract
Conference participation
第一届生物信息学人才发展论坛
present
Zhuhai, CN
2019/7/28 - 2019/7/27
2019年“双一流”农科联盟暨学科建设研讨会
present
Wuhan, CN
2019/7/16
深圳市合成生物产业发展研讨会
present
Shenzhen, CN
2019/6/14
中国肠道大会
present
Beijing, CN
2019/5/6 - 2019/5/4
Sino-German Symposium on Microbiomics and Plant Health
present
Wuhan, CN
2018/9/24
未来组学术研讨会
present
Wuhan, CN
2018/8/8
School Honors
农业微生物学国家重点实验室优秀研究生
10 each year
Wuhan, CN
2012 - 2011
优秀毕业研究生
n.a.
Wuhan, CN
2012
三好研究生
n.a.
Wuhan, CN
2011 - 2010
三好研究生
n.a.
Wuhan, CN
2009 - 2008
优秀毕业生
5 out of 45
Wuhan, CN
2008
三好学生
10 out of 45
Wuhan, CN
2007 - 2006
优秀团员
5 out of 45
Wuhan, CN
2006 - 2005
三好学生
10 out of 45
Wuhan, CN
2005 - 2004
Publifications
- Citation = 539
- H-index = 12
- I10-index = 13
Soil Biofilms: Microbial Interactions, Challenges, and Advanced Techniques for Ex-Situ Characterization
Soil Ecology Letters, 2019, 1(3-4):85-93
N/A
2019
- Cai, Peng; Sun, Xiaojie; Wu, Yichao; Gao, Chun-Hui; Mortimer, Monika; Holden, Patricia A.; Redmile-Gordon, Marc; Huang, Qiaoyun
Cross-Talk between the Three furA Orthologs in Mycobacterium Smegmatis and the Contribution to Isoniazid Resistance
The Journal of Biochemistry, 2019, 166(3):237-243
N/A
- Gao, Chun-Hui; Wei, Wen-Ping; Tao, Hui-Ling; Cai, Li-Kai; Jia, Wan-Zhong; Hu, Lihua; Yang, Min
Impact of Metal Oxide Nanoparticles on in Vitro DNA Amplification
PeerJ, 2019, 7:e7228
N/A
- Gao, Chun-Hui; Mortimer, Monika; Zhang, Ming; Holden, Patricia A.; Cai, Peng; Wu, Shan; Xin, Yuexing; Wu, Yichao; Huang, Qiaoyun
Extraction of Extracellular Polymeric Substances (EPS) from Red Soils (Ultisols)
Soil Biology and Biochemistry, 2019, 135:283-285
N/A
- Wang, Shuang; Redmile-Gordon, Marc; Mortimer, Monika; Cai, Peng; Wu, Yichao; Peacock, Caroline L.; Gao, Chun-Hui; Huang, Qiaoyun
Soil Biofilm Formation Enhances Microbial Community Diversity and Metabolic Activity
Environment International, 2019, 132:105116
N/A
- Wu, Yichao; Cai, Peng; Jing, Xinxin; Niu, Xueke; Ji, Dandan; Ashry, Noha Mohamed; Gao, Chun-Hui; Huang, Qiaoyun
OxiR Specifically Responds to Isoniazid and Regulates Isoniazid Susceptibility in Mycobacteria
FEMS Microbiology Letters, 2019
N/A
- Yang, Min; Zhang, Li; Tao, Hui-Ling; Sun, Yuan-Chao; Lou, Zhong-Zi; Jia, Wan-Zhong; Hu, Li-Hua; Gao, Chun-Hui
Impact of Soil Clay Minerals on Growth, Biofilm Formation, and Virulence Gene Expression of Escherichia Coli O157:H7
Environmental Pollution, 2018, 243:953-960
N/A
2018
- Cai, Peng; Liu, Xing; Ji, Dandan; Yang, Shanshan; Walker, Sharon L.; Wu, Yichao; Gao, Chun-Hui; Huang, Qiaoyun
Co-Culture of Soil Biofilm Isolates Enables the Discovery of Novel Antibiotics
bioRxiv, 2018, 353755
N/A
- Gao, Chun-Hui; Cai, Peng; Li, Zhunjie; Wu, Yichao; Huang, Qiaoyun
Towards a Better Understanding of the Aggregation Mechanisms of Iron (Hydr)Oxide Nanoparticles Interacting with Extracellular Polymeric Substances: Role of pH and Electrolyte Solution
Science of The Total Environment, 2018, 645:372-379
N/A
- Lin, Di; Cai, Peng; Peacock, Caroline L.; Wu, Yichao; Gao, Chun-Hui; Peng, Wanxi; Huang, Qiaoyun; Liang, Wei
Metabolism, Survival, and Gene Expression of Pseudomonas Putida to Hematite Nanoparticles Mediated by Surface-Bound Humic Acid
Environmental Science: Nano, 2018
N/A
- Ouyang, Kai; L. Walker, Sharon; Yu, Xiao-Ying; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng
Recent Advances in Microbial Electrochemical System for Soil Bioremediation
Chemosphere, 2018, 211:156-163
N/A
- Wu, Yichao; Jing, Xinxin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng
Survival of Escherichia Coli O157:H7 in Various Soil Particles: Importance of the Attached Bacterial Phenotype
Biology and Fertility of Soils, 2017, 53(2):209-219
N/A
2017
- Liu, Xing; Gao, Chun-Hui; Ji, Dandan; Walker, Sharon L.; Huang, Qiaoyun; Cai, Peng
Bacillus Subtilis Biofilm Development in the Presence of Soil Clay Minerals and Iron Oxides
npj Biofilms and Microbiomes, 2017, 3(1):4
N/A
- Ma, Wenting; Peng, Donghai; Walker, Sharon L.; Cao, Bin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng
Effects of Humic Acid on the Interactions between Zinc Oxide Nanoparticles and Bacterial Biofilms
Environmental Pollution, 2017
N/A
- Ouyang, Kai; Yu, Xiao-Ying; Zhu, Yunlin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng
Metal-Free Inactivation of E. Coli O157:H7 by Fullerene/C3N4 Hybrid under Visible Light Irradiation
Ecotoxicology and Environmental Safety, 2017, 136:40-45
N/A
- Ouyang, Kai; Dai, Ke; Chen, Hao; Huang, Qiaoyun; Gao, Chun-Hui; Cai, Peng
自然环境中的多物种生物膜:研究方法及社群相互作用
农业资源与环境学报, 2017, (01):6-14
N/A
- 孙晓洁; 高春辉; 黄巧云; 蔡鹏
大肠杆菌表面感应机制研究进展
浙江大学学报(农业与生命科学版), 2017, (06):685-690
N/A
- 王立亮; 高春辉; 吴一超; 黄巧云; 蔡鹏
Identification and Functional Study of Type III-A CRISPR-Cas Systems in Clinical Isolates of Staphylococcus Aureus
International Journal of Medical Microbiology, 2016, 306(8):686-696
N/A
2016
- Cao, Linyan; Gao, Chun-Hui; Zhu, Jiade; Zhao, Liping; Wu, Qingfa; Li, Min; Sun, Baolin
Identification of Genetic Variations Associated with Epsilon-Poly-Lysine Biosynthesis in Streptomyces Albulus ZPM by Genome Sequencing
Scientific Reports, 2015, 5:9201
N/A
2015
- Wang, Lin; Gao, Chun-Hui; Tang, Nan; Hu, Songnian; Wu, Qingfa
InbR, a TetR Family Regulator, Binds with Isoniazid and Influences Multidrug Resistance in Mycobacterium Bovis BCG
Scientific Reports, 2015, 5:13969
N/A
- Yang, Min; Gao, Chun-Hui; Hu, Jialing; Zhao, Lei; Huang, Qiaoyun; He, Zheng-Guo
Characterization of the Interaction between a SirR Family Transcriptional Factor of Mycobacterium~Tuberculosis, Encoded by Rv2788, and a Pair of Toxin-Antitoxin Proteins RelJ/K, Encoded by Rv3357 and Rv3358
The FEBS journal, 2014, 281(12):2726-2737
N/A
2014
- Yang, Min; Gao, Chun-Hui; Hu, Jialing; Dong, Chao; He, Zheng-Guo
A Novel marRAB Operon Contributes to the Rifampicin Resistance in Mycobacterium Smegmatis
PLoS ONE, 2014, 9(8):e106016
N/A
- Zhang, Haiwei; Gao, Long; Zhang, Jiaoling; Li, Weihui; Yang, Min; Zhang, Hua; Gao, Chun-Hui; He, Zheng-Guo
Characterization of a Novel ArsR-Like Regulator Encoded by Rv2034 in Mycobacterium Tuberculosis
PloS One, 2012, 7(4):e36255
N/A
2012
- Gao, Chun-Hui; Yang, Min; He, Zheng-Guo
A TetR-like Regulator Broadly Affects the Expressions of Diverse Genes in Mycobacterium Smegmatis
Nucleic Acids Research, 2012, 40(3):1009-1020
N/A
- Yang, Min; Gao, Chun-Hui; Cui, Tao; An, Jingning; He, Zheng-Guo
An ArsR-like Transcriptional Factor Recognizes a Conserved Sequence Motif and Positively Regulates the Expression of phoP in Mycobacteria
Biochemical and Biophysical Research Communications, 2011, 411(4):726-731
N/A
2011
- Gao, Chun-Hui; Yang, Min; He, Zheng-Guo
Global Protein-Protein Interaction Network in the Human Pathogen Mycobacterium Tuberculosis H37Rv
Journal of Proteome Research, 2010, 9(12):6665-6677
N/A
2010
- Wang, Yi; Cui, Tao; Zhang, Cong; Yang, Min; Huang, Yuanxia; Li, Weihui; Zhang, Lei; Gao, Chun-Hui; He, Yang; Li, Yuqing; Huang, Feng; Zeng, Jumei; Huang, Cheng; Yang, Qiong; Tian, Yuxi; Zhao, Chunchao; Chen, Huanchun; Zhang, Hua; He, Zheng-Guo
Characterization of the Interaction and Cross-Regulation of Three Mycobacterium Tuberculosis RelBE Modules
PLoS ONE, 2010, 5(5):e10672
N/A
- Yang, Min; Gao, Chun-Hui; Wang, Yi; Zhang, Hua; He, Zheng-Guo
Dissecting Transcription Regulatory Pathways through a New Bacterial One-Hybrid Reporter System
Genome Research, 2009, 19(7):1301-1308
N/A
2009
- Guo, Manman; Feng, Hui; Zhang, Jun; Wang, Wenqin; Wang, Yi; Li, Yuqing; Gao, Chun-Hui; Chen, Huanchun; Feng, Ying; He, Zheng-Guo
Archaeal Eukaryote-like Orc1/Cdc6 Initiators Physically Interact with DNA Polymerase B1 and Regulate Its Functions
Proceedings of the National Academy of Sciences, 2009, 106(19):7792-7797
N/A
- Zhang, Lu; Zhang, Lei; Liu, Yi; Yang, Shifan; Gao, Chun-Hui; Gong, Hongchao; Feng, Ying; He, Zheng-Guo